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apbsmem a graphical interface for electrostatic calculations at the membraneapbsmem静电膜计算的图形界面.pdf

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apbsmem a graphical interface for electrostatic calculations at the membraneapbsmem静电膜计算的图形界面

APBSmem: A Graphical Interface for Electrostatic Calculations at the Membrane 1 1 2 3 4 Keith M. Callenberg , Om P. Choudhary , Gabriel L. de Forest , David W. Gohara , Nathan A. Baker , Michael Grabe2,5* 1 Carnegie Mellon-University of Pittsburgh Program in Computational Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America, 2 Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America, 3 The Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University, St. Louis, Missouri, United States of America, 4 Pacific Northwest National Laboratory, Richland, Washington, United States of America, 5 Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America Abstract Electrostatic forces are one of the primary determinants of molecular interactions. They help guide the folding of proteins, increase the binding of one protein to another and facilitate protein-DNA and protein-ligand binding. A popular method for computing the electrostatic properties of biological systems is to numerically solve the Poisson-Boltzmann (PB) equation, and there are several easy-to-use software packages available that solve the PB equation for soluble proteins. Here we present a freely available program, called APBSmem, for carrying out these calculations in the presence of a membrane. The Adaptive Poisson-Boltzmann Solver (APBS) is used as a back-end for solving the PB equation, and a Java-based graphical user interface (GUI) coordinates a set of routines that introduce the influence of the membrane, determine its placement relative to the protein, and set the membrane p